How To Install sambamba on Ubuntu 18.04
Introduction
In this tutorial we learn how to install sambamba on Ubuntu 18.04.
What is sambamba
sambamba is:
Sambamba positions itself as a performant alternative to samtools and provides tools for
- Powerful filtering with sambamba view –filter
- Picard-like SAM header merging in the merge tool
- Optional for operations on whole BAMs
- Fast copying of a region to a new file with the slice tool
- Duplicate marking/removal, using the Picard criteria
There are three methods to install sambamba on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install sambamba Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install sambamba using apt-get by running the following command:
sudo apt-get -y install sambamba
Install sambamba Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install sambamba using apt by running the following command:
sudo apt -y install sambamba
Install sambamba Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install sambamba using aptitude by running the following command:
sudo aptitude -y install sambamba
How To Uninstall sambamba on Ubuntu 18.04
To uninstall only the sambamba package we can use the following command:
sudo apt-get remove sambamba
Uninstall sambamba And Its Dependencies
To uninstall sambamba and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove sambamba
Remove sambamba Configurations and Data
To remove sambamba configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge sambamba
Remove sambamba configuration, data, and all of its dependencies
We can use the following command to remove sambamba configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge sambamba
References
Summary
In this tutorial we learn how to install sambamba package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
